Sodium in PDB 5trd: Structure of Rbkr (Riboflavin Kinase) From Thermoplasma Acidophilum Determined in Complex with Ctp and Its Cognate Dna Operator

All present enzymatic activity of Structure of Rbkr (Riboflavin Kinase) From Thermoplasma Acidophilum Determined in Complex with Ctp and Its Cognate Dna Operator:
2.7.1.161;

The structure of Structure of Rbkr (Riboflavin Kinase) From Thermoplasma Acidophilum Determined in Complex with Ctp and Its Cognate Dna Operator, PDB code: 5trd was solved by M.W.Vetting, I.A.Rodionova, X.Li, A.L.Osterman, D.A.Rodionov, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.98 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.411, 95.040, 61.262, 90.00, 113.51, 90.00
R / Rfree (%)	17.4 / 21.7

The binding sites of Sodium atom in the Structure of Rbkr (Riboflavin Kinase) From Thermoplasma Acidophilum Determined in Complex with Ctp and Its Cognate Dna Operator (pdb code 5trd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Rbkr (Riboflavin Kinase) From Thermoplasma Acidophilum Determined in Complex with Ctp and Its Cognate Dna Operator, PDB code: 5trd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Rbkr (Riboflavin Kinase) From Thermoplasma Acidophilum Determined in Complex with Ctp and Its Cognate Dna Operator


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Rbkr (Riboflavin Kinase) From Thermoplasma Acidophilum Determined in Complex with Ctp and Its Cognate Dna Operator within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:19.3 occ:1.00 O1B A:CTP301 2.2 23.0 1.0 O1A A:CTP301 2.3 18.9 1.0 O A:THR131 2.3 19.7 1.0 O1G A:CTP301 2.3 25.6 1.0 OD1 A:ASN133 2.4 19.8 1.0 OG1 A:THR131 2.4 20.0 1.0 PB A:CTP301 3.1 23.0 1.0 C A:THR131 3.2 19.5 1.0 PG A:CTP301 3.3 32.4 1.0 CG A:ASN133 3.3 27.4 1.0 PA A:CTP301 3.4 22.3 1.0 O3B A:CTP301 3.5 24.7 1.0 CB A:THR131 3.5 18.9 1.0 O3A A:CTP301 3.6 24.8 1.0 CA A:THR131 3.6 18.6 1.0 ND2 A:ASN133 3.7 32.9 1.0 N A:THR131 3.7 18.4 1.0 O2G A:CTP301 3.7 34.1 1.0 OE2 A:GLU195 3.8 40.0 1.0 O A:HOH450 4.0 17.7 1.0 O5' A:CTP301 4.1 21.5 1.0 O A:HOH408 4.2 37.3 1.0 O A:HOH440 4.2 26.3 1.0 N A:LEU132 4.3 18.9 1.0 N A:ASN133 4.4 19.5 1.0 CA A:GLY106 4.4 24.2 1.0 O2B A:CTP301 4.5 26.0 1.0 N A:GLY106 4.5 25.4 1.0 O A:HOH451 4.6 33.0 1.0 O2A A:CTP301 4.6 27.4 1.0 CB A:ASN133 4.7 17.5 1.0 O3G A:CTP301 4.7 37.8 1.0 CG2 A:THR131 4.7 16.9 1.0 C A:LEU132 4.7 23.6 1.0 CD A:GLU195 4.8 39.4 1.0 CA A:LEU132 4.8 19.6 1.0 CA A:ASN133 4.9 19.1 1.0 C A:GLY130 5.0 19.8 1.0 C2' A:CTP301 5.0 16.3 1.0

Sodium binding site 2 out of 2 in the Structure of Rbkr (Riboflavin Kinase) From Thermoplasma Acidophilum Determined in Complex with Ctp and Its Cognate Dna Operator


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Rbkr (Riboflavin Kinase) From Thermoplasma Acidophilum Determined in Complex with Ctp and Its Cognate Dna Operator within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:22.0 occ:1.00 O2B B:CTP301 2.2 26.3 1.0 O B:THR131 2.2 18.7 1.0 OG1 B:THR131 2.3 19.3 1.0 O2A B:CTP301 2.4 21.9 1.0 OD1 B:ASN133 2.5 24.1 1.0 O2G B:CTP301 2.5 31.8 1.0 C B:THR131 3.1 19.8 1.0 PB B:CTP301 3.2 27.1 1.0 CG B:ASN133 3.3 35.1 1.0 PG B:CTP301 3.3 37.8 1.0 ND2 B:ASN133 3.4 57.0 1.0 CB B:THR131 3.4 18.1 1.0 PA B:CTP301 3.5 24.3 1.0 O3G B:CTP301 3.5 50.5 1.0 O3B B:CTP301 3.5 26.6 1.0 CA B:THR131 3.6 17.4 1.0 N B:THR131 3.7 17.9 1.0 O3A B:CTP301 3.7 26.3 1.0 OE2 B:GLU195 3.7 31.6 1.0 O B:HOH441 3.8 19.3 1.0 O B:HOH405 3.9 36.1 1.0 O5' B:CTP301 4.2 26.0 1.0 CA B:GLY106 4.2 26.8 1.0 N B:GLY106 4.2 21.8 1.0 O B:HOH468 4.3 31.1 1.0 N B:LEU132 4.3 18.3 1.0 N B:ASN133 4.3 18.4 1.0 CD B:GLU195 4.5 28.9 1.0 O1B B:CTP301 4.5 31.8 1.0 CB B:ASN133 4.6 26.3 1.0 CG2 B:THR131 4.6 17.0 1.0 OE1 B:GLU195 4.7 32.1 1.0 O1A B:CTP301 4.7 22.2 1.0 C B:LEU132 4.7 25.2 1.0 O1G B:CTP301 4.7 56.9 1.0 CA B:LEU132 4.7 19.1 1.0 C2' B:CTP301 4.9 20.4 1.0 CA B:ASN133 4.9 19.9 1.0 C B:GLY130 5.0 19.8 1.0

M.W.Vetting, I.A.Rodionova, X.Li, A.L.Osterman, D.A.Rodionov, S.C.Almo. Structure of Rbkr (Riboflavin Kinase) From Thermoplasma Acidophilum Determined in Complex with Ctp and Its Cognate Dna Operator To Be Published.